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Katz received BS degrees in mathematics and chemistry from MIT in 1996, followed by a master's degree in chemistry from Columbia University in 1998. After transferring to the computer science department, he received M.Phil. and PhD degrees in computer science from Columbia University in 2001 and 2002, respectively. While in graduate school, he worked as a research scientist at Telcordia Technologies (now ACS). He has been on the faculty of the University of Maryland since 2002.

He has held visiting positions at UCLA, IBM T.J. Watson Research Center, and the Ecole Normale Superieure. He was a member of the DARPA Computer Science Study Group in 2009-2010.[5] He also works as a consultant in the fields of cryptography and computer security.

He received the Humboldt Research Award to support collaborative research with colleagues in Germany during 2015.[6] He also received the University of Maryland "Distinguished Scholar-Teacher" award in 2017.[7] In 2019 Katz was named an IACR Fellow for his research contributions in public-key cryptography and cryptographic protocols along with service and education contributions to the cryptographic field.[8]

Katz has worked on various aspects of cryptography, computer security, and theoretical computer science. His doctoral thesis was on designing protocols secure against man-in-the-middle attacks, most notably describing an efficient protocol for password-based authenticated key exchange.[9] He has also worked in the areas of secure multi-party computation,[10] public-key encryption,[11] and digital signatures.[12] He has served on the program committees of numerous conferences, including serving as co-program chair for the annual Crypto conference in 2016 and 2017 and co-program chair for the ACM Conference on Computer and Communications Security in 2019-2020. He is also currently an editor of the Journal of Cryptology,[13] the premier journal of the field.

He has written two books: a textbook on modern cryptography (with Yehuda Lindell) that is used in many universities around the world,[14]
and a monograph on digital signature schemes.

Jonathan Katz and Yehuda Lindell (2007). Introduction to Modern Cryptography. Chapman and Hall. ISBN978-1584885511. According to WorldCat, the book is held in 310 libraries.[15] The second edition of this book was published in 2014.